############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data GeomxTools ### ############################################################################## ############################################################################## * checking for file ‘GeomxTools/DESCRIPTION’ ... OK * preparing ‘GeomxTools’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’ using rmarkdown Loading required package: Biobase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: ggplot2 Registered S3 method overwritten by 'GGally': method from +.gg ggplot2 Attaching package: 'EnvStats' The following objects are masked from 'package:stats': predict, predict.lm The following object is masked from 'package:base': print.default --- finished re-building ‘Developer_Introduction_to_the_NanoStringGeoMxSet.Rmd’ --- re-building ‘GeomxSet_coercions.Rmd’ using rmarkdown Attaching SeuratObject Attaching sp Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |=================================== | 50% | |======================================================================| 100% Warning in irlba(A = t(x = object), nv = npcs, ...) : You're computing too large a percentage of total singular values, use a standard svd instead. Computing nearest neighbor graph Computing SNN Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation' This message will be shown once per session 21:49:47 UMAP embedding parameters a = 0.9922 b = 1.112 21:49:47 Read 83 rows and found 30 numeric columns 21:49:47 Using Annoy for neighbor search, n_neighbors = 30 21:49:47 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 21:49:47 Writing NN index file to temp file /tmp/Rtmpb2v71Z/file6f49cd66aac 21:49:47 Searching Annoy index using 1 thread, search_k = 3000 21:49:47 Annoy recall = 100% 21:49:48 Commencing smooth kNN distance calibration using 1 thread 21:49:49 Initializing from normalized Laplacian + noise 21:49:49 Commencing optimization for 500 epochs, with 1430 positive edges 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 21:49:50 Optimization finished Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |=================================== | 50% | |======================================================================| 100% Computing nearest neighbor graph Computing SNN 21:49:52 UMAP embedding parameters a = 0.9922 b = 1.112 21:49:52 Read 199 rows and found 30 numeric columns 21:49:52 Using Annoy for neighbor search, n_neighbors = 30 21:49:52 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 21:49:52 Writing NN index file to temp file /tmp/Rtmpb2v71Z/file6f49713165b3 21:49:52 Searching Annoy index using 1 thread, search_k = 3000 21:49:52 Annoy recall = 100% 21:49:53 Commencing smooth kNN distance calibration using 1 thread 21:49:54 Initializing from normalized Laplacian + noise 21:49:54 Commencing optimization for 500 epochs, with 7298 positive edges 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 21:49:55 Optimization finished Quitting from lines 313-314 (GeomxSet_coercions.Rmd) Error: processing vignette 'GeomxSet_coercions.Rmd' failed with diagnostics: there is no package called 'SpatialExperiment' --- failed re-building ‘GeomxSet_coercions.Rmd’ --- re-building ‘Protein_in_GeomxTools.Rmd’ using rmarkdown `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. --- finished re-building ‘Protein_in_GeomxTools.Rmd’ SUMMARY: processing the following file failed: ‘GeomxSet_coercions.Rmd’ Error: Vignette re-building failed. Execution halted